Research workbench
Crystal structure of trmd, a tRNA-(N1G37) methyltransferase, from mycobacterium abscessus in complex with inhibitor
Analyse Crystal structure of trmd, a tRNA-(N1G37) methyltransferase, from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QQW
- Type
- protein
- Length
- 411 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (guanine-N(1)-)-methyltransferase
- EC
- 2.1.1.228
- UniProt
- B1MDI3
- Ligands
- JDQ, SO4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 212 | 39% helix, 21% strand | B1MDI3 |
| B | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 199 | 37% helix, 23% strand | B1MDI3 |
Ligands and binding sites
- JDQ · 3-[1-(phenylmethyl)indol-6-yl]-1~{H}-pyrazol-5-amine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.72 | 0.85 | 47 | JDQ |
| 2 | 319 | 0.72 | 0.85 | 55 | JDQ |
| 3 | 197 | 0.50 | 0.77 | 27 | empty |
| 4 | 93 | 0.39 | 0.77 | 20 | empty |
| 5 | 56 | 0.33 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3530 Ų buried · 79 hydrogen bonds · protein-protein
Compared structures
- 6QQW · Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt B1MDI3
- Elsewhere: RCSB PDB 6QQW · PDBe 6QQW · UniProt B1MDI3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.